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Last data update: 2014.03.03

R: Method implementing Lattice ECDF plots for flow data

prepanel.ecdfplot.flowset

R Documentation

Method implementing Lattice ECDF plots for flow data

Description

This function creates Trellis displays of Empirical Cumulative Distribution Functions from flow cytometry data using a formula interface.

Usage

prepanel.ecdfplot.flowset(x, frames, channel, f.value, ...)

panel.ecdfplot.flowset(x, frames, channel, f.value, ref = TRUE,
  groups = NULL, subscripts, col = superpose.symbol$col, col.points = col,
  pch = superpose.symbol$pch, cex = superpose.symbol$cex,
  alpha = superpose.symbol$alpha, col.line = col,
  lty = superpose.line$lty, lwd = superpose.line$lwd, ...)

## S4 method for signature 'formula,flowSet'
ecdfplot(x, data, xlab, f.value = function(n)
  ppoints(ceiling(sqrt(n))), prepanel = prepanel.ecdfplot.flowset,
  panel = panel.ecdfplot.flowset, type = "l", as.table = TRUE, ...)

Arguments

`x`	a formula describing the structure of the plot and the variables to be used in the display. For the prepanel and panel functions, a vector of names for the flow frames to be used in the panel.
`frames`	environment containing frame-specific data
`channel`	expression involving names of columns in the data
`f.value`	determines the number of points used in the plot `ecdfplot` for details.
`ref`	logical; whether to add reference lines at 0 and 1
`groups,subscripts`	grouping variable, if specified, and subscripts indexing which frames are being used in the panel. See `xyplot` for details.
`col,col.points,pch,cex,alpha,col.line,lty,lwd`	vector of graphical parameters that are replicated for each group
`data`	a `flowSet` object that serves as a source of data
`xlab`	Labels for data axes, with suitable defaults taken from the formula
`panel,prepanel`	the panel and prepanel functions.
`type`	type of rendering; by default lines are drawn
`as.table`	logical; whether to draw panels from top left
`...`	more arguments, usually passed on to the underlying lattice methods and the panel function.

Methods

ecdfplot: signature(x = "formula", data = "flowSet"): plote empirical CDF for a given channel, with one or more samples per panel

Examples

data(GvHD)

ecdfplot(~ `FSC-H` | Patient, GvHD, f.value = ppoints(100))

ecdfplot(~ asinh(`FSC-H`) | Patient, GvHD,
         strip = strip.custom(strip.names = TRUE),
         ref = FALSE)

ecdfplot(~ asinh(`FSC-H`) | Patient, GvHD, groups = Visit,
         strip = strip.custom(strip.names = TRUE),
         ref = FALSE, auto.key = list(columns = 4))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(flowViz)
Loading required package: flowCore
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowViz/ecdfplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: prepanel.ecdfplot.flowset
> ### Title: Method implementing Lattice ECDF plots for flow data
> ### Aliases: ecdfplot ecdfplot,formula,flowSet-method
> ###   panel.ecdfplot.flowset prepanel.ecdfplot.flowset
> ### Keywords: dplot methods
> 
> ### ** Examples
> 
> data(GvHD)
> 
> ecdfplot(~ `FSC-H` | Patient, GvHD, f.value = ppoints(100))
> 
> ecdfplot(~ asinh(`FSC-H`) | Patient, GvHD,
+          strip = strip.custom(strip.names = TRUE),
+          ref = FALSE)
> 
> ecdfplot(~ asinh(`FSC-H`) | Patient, GvHD, groups = Visit,
+          strip = strip.custom(strip.names = TRUE),
+          ref = FALSE, auto.key = list(columns = 4))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>